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Phylogenetic and non-phylogenetic patterns in the richness, frequency and composition of links in a herbivore-parasitoid interaction network
No full textRevealing processes that structure species interactions is central to understanding community assembly and dynamics. Species interact via their phenotypes, but identifying and quantifying the traits that structure species-specific interactions (links) can be challenging. Where these traits show phylogenetic signal, however, link properties may be predictable using models that incorporate phylogenies in place of trait data. We analysed variation in link richness, frequency, and species identity in a multi-site dataset of interactions between oak cynipid galls and parasitoid natural enemies, using a Bayesian mixed modelling framework allowing concurrent fitting of phylogenetic effects of both trophic levels. In both link incidence (presence/absence) and link frequency datasets, we identified strong signatures of cophylogeny (related parasitoids attack related host galls) alongside patterns independent of either phylogeny. Our results are robust to simulations of substantially reduced sample completeness, and are consistent with the structuring of trophic interactions by a combination of phylogenetically conserved and convergently evolving traits in both trophic levels. We discuss our results in light of phenotypic traits thought to structure gall-parasitoid interactions and consider wider applications of this approach, including inference of underlying community assembly processes and prediction of economically important trophic interactions
Klebsiella variicola dataset
No full textThis dataset of Klebsiella variicola contains 715 genome files categorised as human, animal, plant or environmental-associated strains. This dataset was used to study the population structure, evolutionary dynamics, resistance and virulence profiles of Klebsiella variicola
Brain Lymphatics Measurements from MRI - Guidelines
No full textThe process detailed in this document is associated with a published investigation into semi-quantitatively measuring and visualising brain fluid pathways, including meningeal lymphatics, using magnetic resonance imaging (MRI) - Sennfalt et al., (2023) DOI:10.1177/0271678X231179555. This document describes the procedures to be carried out for measuring signal intensity on 2D coronal T2-FLAIR MRI in regions of interest (ROIs) relevant to meningiolymphatic brain clearance as per current knowledge. It adds 8 ROIs to the 7 ROIs described in Sennfalt et al., (2023), selected from a combination of: a) literature review and b) radiological examination of contrast enhanced regions on T2-FLAIR scans and T2-weighted scans to ensure FLAIR-specific contrast isolation. It also details the criteria for scoring the signal intensity in the ROIs. Visualisation to derive these guidelines used a Philips Carestream DICOM viewing software (© 2022 Koninklijke Philips N.V., version 12.2.5.00397), a typical and widely used clinical radiological viewing platform
High Resolution sections of eMouseAtlas Models: EMA220, Theiler Stage 12 TS12 (cultured)- Embryo
No full textHigh resolution images of each section used for the Mouse Atlas 3D models. Images are sub-sampled for the 3D models to provide approximately iso-tropic voxel dimensions, here the images are at the full resolution of the original digitisation
High Resolution sections of eMouseAtlas Models: EMA105, Theiler Stage 23 TS23(15 dpc) - Kidney
No full textHigh resolution images of each section used for the Mouse Atlas 3D models. Images are sub-sampled for the 3D models to provide approximately iso-tropic voxel dimensions, here the images are at the full resolution of the original digitisation
High Resolution sections of eMouseAtlas Models: EMA17, Theiler Stage 11 TS11(7.5 dpc)
No full textHigh resolution images of each section used for the Mouse Atlas 3D models. Images are sub-sampled for the 3D models to provide approximately iso-tropic voxel dimensions, here the images are at the full resolution of the original digitisation
Individual Animal Serological Test Results From Antibody Screening of Tanzanian Dairy Cattle to Brucellosis, Leptospirosis, Q Fever, Rift Valley Fever, Neospora Caninum, and Toxoplasma Gondii
No full textData from paper provisionally accepted in Frontiers Genetics - Livestock Genomics. Research topic Advances in Livestock Genetics: Enhancing Breeding Practices and Improving Animal Health.
"Genetic estimates and genome-wide association studies of antibody responses in Tanzanian dairy cattle." Luis E Hernandez-Castro, Elizabeth Anne Jessie Cook, Oswald Matika, Isaac Joseph Mengele, Shabani Kiyabo Motto, Shedrack Festo Bwatota, Bibiana Zirra-Shallangwa, Ricardo Pong-Wong, James Prendergast, Raphael Mrode, Philip G Toye, Daniel Mushumbusi Komwihangilo, Eliamoni Lyatuu,Benedict E Karani, Getrude Nangekhe, Okeyo Ally Mwai, Gabriel Mkilema Shirima, and Barend Mark de Clare Bronsvoort.
Identifying the genetic determinants of host defence against infectious pathogens is central to enhancing disease resilience and therapeutic efficacy in livestock. Here, we investigated immune response heritability to important infectious diseases affecting dairy smallholder cattle using variance component analysis. We also conducted genome-wide association studies (GWAS) to identify genetic variants that may help understand the underlying biology of these health traits. Assessing 668,911 single-nucleotide polymorphisms (SNP) genotyped in 2045 crossbreed cattle sampled from six regions of Tanzania, we identified high levels of interregional admixture and European introgression, which may increase infectious disease susceptibility relative to indigenous breeds. Heritability estimates were low to moderate, ranging from 0.03 (SE ± 0.06) to 0.44 (SE ± 0.07), depending on the health trait. GWAS results revealed several loci associated with seropositivity to the viral diseases Rift Valley fever and bovine viral diarrhoea, the protozoan parasites Neospora caninum and Toxoplasma gondii, and the bacterial pathogens Brucella sp, Leptospira hardjo and Coxiella burnetti. The identified quantitative trait loci mapped to genes involved in immune defence, tumour suppression, neurological processes, and cell exocytosis. We propose that our results form a baseline in the future understanding of the cellular pathways contributing to general and taxon-specific infection responses, and to advance selective breeding and therapeutic target designs.
The serological response trait was obtained for each individual animal through testing for antibody response to seven pathogens using commercial ELISA kits of bovine viral diarrhoea virus (ID Screen® BVD p80 Antibody Competition, Innovate Diagnostics, France), Neospora caninum (ID Screen® Neospora caninum Competition, Innovate Diagnostics, France), Leptospira hardjo (Leptospira interrogans subtype Hardjoprajitno and Leptospira borgpetersenii subtype Hardjobovis; The Linnodee Leptospira Hardjo ELISA KitTM, Linnodee Animal Care, UK), Rift Valley fever virus (ID Screen® Rift Valley Fever Competition Multi-species, Innovate Diagnostics, France), Toxoplasma gondii (ID Screen® Toxoplasmosis Indirect Multi-species, Innovate Diagnostics, France), Coxiella burnetii (Q fever; PrioCHECKIT™ Ruminant Q Fever Ab Plate Kit, Thermofisher Scientific, USA) and Brucella abortus (COMPELISA 160 & 400, APHA Scientific, UK). Following manufacturer guidelines. All optical density (OD) values were transformed into a binary seropositive seronegative classification based on the manufacturers recommended cut-offs
Semi-Automated layer-by-layer biofabrication using Rotational Internal Flow Layer Engineering technology
No full textThe automation of biofabrication processes has the potential to increase both the scale and reproducibility of human tissue production for replacing animal usage in research and ultimately clinical use. The biofabrication technology, Rotational Internal Flow Layer Engineering (RIFLE), produces layered tubular constructs with a resolution commensurate with the microscale strata observed in many human tissue types. The previously published RIFLE process required liquid phase cell-laden hydrogels to be manually applied onto the inner surface of a high-speed rotating mould. Here we describe improvement of the RIFLE system by automating elements of the process, in particular the liquid dispensing element, and present the use of this system for two commonly used biofabrication hydrogels; alginate and collagen. Semi-automatically assembled cell layers matched the viabilities of those produced manually, with automated collagen demonstrating the highest viabilities (>91%) over the 10 days measured, highlighting its advantages as a material for tissue engineering applications. The encapsulation of labelled cells in predefined collagen layer patterns confirmed that the semi-automated RIFLE system was able to assemble separate cell populations in cell-width layers (≈14µm). Semi-automated dosing reduced the manual operations in the RIFLE process, reducing the workload on researchers and minimising the opportunity for human error. Further opportunity exists for higher levels of automation in the overall process, particularly needed in the preparation of cell-hydrogel suspensions, a common manual labour-intensive process in many biofabrication technologies
Codes and supplemental data for 'Phloem evolution in ferns was shaped by phylogeny and records a trend of decreasing conductivity through geological time'
No full textThe phloem, the sugar-transporting tissue in vascular plants, is one of the most important but least well characterised plant tissues from an evolutionary perspective. Here we substantially extend the evidence for phloem evolution using ferns as a case study due to their long evolutionary history and famed vascular diversity. We carried out a comparative histological investigation of the conducting cells of the phloem, termed sieve elements, in 26 extant species, spanning 21 families and making over 18,000 measurements. We found that sieve element radius correlates with vascular bundle radius and leaf area, but that these correlations alone didn’t account for the observed diversity in sieve element radii. Instead, sieve element radius preserves a strong phylogenetic signal and is similar in closely related taxa despite differences in leaf and vascular characteristics. Next, by combining evidence from extinct and extant species, we recognised a trend of decreasing sieve element radius and total conducting area through geological time. We predict that this decrease resulted in reduced phloem conductivity especially in the eupolypod ferns that diversified into angiosperm-dominated ecosystems. Our findings demonstrate that phloem structure has changed over the long evolutionary history of ferns and that this likely had an important functional impact.R scripts and source data used to produce the result figures. Images used to collect data on sieve element radius, sieve element numbers, leaf and vascular traits. Image files are named with the initial two letters of the genus name and the initial two letters of the specific epithet. For example, Ceratopteris richardii is abbreviated to CeRi for the image files
Videos of eMouseAtlas Models: Theiler Stage 23 (15 dpc)
No full textA number of videos for each of the eMouseAtlas 3D mouse embryo models to show the overall form and in some cases selected anatomy. Each video is identified by the unique EMA ID with annotation if required. The videos labelled as "watermovies" are captured using the OPT system with the embryo spun on a longitudinal axis with no tissue clearing